New water test shows promise for ranches and beaches (Point Reyes Light, 11.26.2008)

Marin County beach

A technology originally invented to detect airborne terrorist pathogens could now help beach-goers, ranchers and shellfish growers throughout West Marin.

A new type of molecular biology gadget called the PhyloChip can differentiate between 32,000 types of bacteria. It’s being used to study bacteria in coastal waters through Marin County’s Clean Beach PhyloChip Project and could have huge implications for water quality tests.

“We’re adding clarity to the whole pollution picture,” said John Hulls, coordinator of the project. “The PhyloChip will show if there is a relationship between current bacterial indicators and harmful pathogens.”

Soon, the PhyloChip may also help the local agricultural community. California state law requires that popular beaches be tested for the presence of bacteria weekly during the main season from April through October. Yet today’s water quality tests were developed around 1900 by Alfred MacConkey for the Royal Commission on Sewage Disposal in London.

When that test shows bacteria counts are too high, beaches are closed and shellfish harvests are shut down. And the closures—which sometimes are unnecessary—often get blamed on cattle and dairy ranchers who then need to pay for mitigation. “Instead of blaming the ranchers for shutting down oysters, the health department really should look at what’s causing the problem,” said Phyllis Faber, a founder of the Marin Agricultural Land Trust.

“When there is an exceedance, there can be finger-pointing,” said Eric Dubinsky, a Lawrence Berkeley National Laboratory postdoctoral fellow with the project. “We think we can develop a test to determine whether or not the source is the cow pasture or the sewage leak park upstream.”

This research is something ranchers are looking forward to. “They would rather see scientific evidence backing up the accusation before they spend a lot of money making improvements,” said Nancy Scolari from Marin County Resource Conservation District. “They want to know if there really is a problem and if they’re causing it,” Hulls added.


The hopes for the PhyloChip Project are ambitious—a complete microbial census and how it changes with time, better keystone indicator bacteria for harmful pathogens, and ultimately a simple, inexpensive test for beach water quality. The project was selected for funding from the Clean Beach Initiative Grant Program, according to Laura Peters of the State Water Resources Control Board.

“We can identify the harmful bacteria and we’re also looking at contamination sources,” said Gary Andersen of Lawrence Berkeley Laboratory, who developed the PhyloChip.

What is the health risk, if any, at a beach after a storm or on a beach near agriculture and sewage lines? Right now, answering that question means using an slow, outdated culture method where water samples are smeared on an agar growth medium and bacteria reproduce under conditions different from those they actually live in. It looks at a limited number of bacteria as indicators for a broad array of sources, some harmful to humans and some not—providing results that lead to potentially unnecessary beach closures and ranch restrictions.

Less than a percent of all bacteria have ever been cultured, and many can never be cultured since they live in a complex microbial community—the microbial biome that Andersen hopes will be examined comprehensively for the first time, using this new tool.

For example, the culture-based test uses E. coli as an indicator of human sewage pollution, though the two are not necessarily related. A 2005 study suggested that the risk of illness was uncorrelated with levels of the traditional water quality indicators—enterococcus and coliforms (such as E. coli). The PhyloChip team hopes to determine which of the thousands of bacteria measured are actually the accurate warning signs of poor water quality, according to Dubinsky.

“If you just measure E. coli, then it could be from any mammal,” said Hulls. “We’re looking for a suite of bacteria that will tell us for sure whether it’s from human sewage or something else like cattle or natural sources.” Current tests don’t discriminate between sources—bacteria from an animal may not be harmful if they don’t cross over to humans. “Bacteria that live in cow poop are different from bacteria that live in human poop,” said Andersen. “But since we can see 32,000 bacteria, we can get a fingerprint of the contamination,” Dubinsky added.

The PhyloChip offers the possibility of a complete census of bacteria in coastal waters. It also offers speedy results compared to the traditional cultures that can take a full day to complete. “You can test the beaches and see what’s in the water on the same day,” said Dubinsky. “So you don’t have to wait overnight before you alert the public.”


The technology was invented in 2000 for Homeland Security to detect airborne terrorist pathogens. At that time, it could look at a few thousand organisms. The latest version, dubbed G3, has 1.1 million probes (or tests) to monitor about 32,000 different types of bacteria.

“Before, we could only get information on a couple organisms in a lot of samples or a lot of organisms in a couple samples,” said Dubinsky. “Now, it’s 32,000 organisms in a thousand samples. It’s so much more information than has ever been collected.”

For every beach water sample, the team will look for and amplify a specific gene that is found in all bacteria. Then that is put onto the PhyloChip, scanned with a laser, and used to reveal all bacteria types present.

Another main goal is to find the sources of contamination. With the PhyloChip, the team can pinpoint exactly where the beach pollution comes from—whether it’s from domestic animals, wild animals or humans. “If it turns out that there’s animal pathogens, it may not warrant beach closures,” said Andersen, adding that the closures would only happen when there’s a real risk for human disease. “If the warning system can define a real risk, people are more likely to heed the signs.”

All the exciting results will be coming out over the next year. In 2010, the ideas could meet reality. The immediate short term objective is to better understand what indicative pathogens are in the beach environments. Then a simple inexpensive test can be developed for county personnel to assess in real-time beach safety. “The ultimate test is to see if people got sick when your test showed positive,” Hulls said. “It’ll prove our chip’s ability to predict whether water is safe or not.”

The project has just finished its first round of beach water quality testing and is awaiting more tweaks. The team has samples from nine beaches between Bodega Bay and San Francisco, and it looked most intensively at Muir Beach and two others that have been listed on the “Beach Bummer” list—the worst California beaches based on their dry weather water quality.

In order to see how the microbial environment changes over time and with the tide, the team conducted high-intensity studies at those three beaches. “How representative are the weekly samples of actual conditions?” Dubinsky asked. Preliminary analyses are showing more variability than was previously thought.

The team stayed at the beaches overnight, taking samples every hour from 10 p.m. until after noon on the next day. Each time, they would wade ankle deep into the water and reach out a painter’s pole with a liter bottle at the end to grab a sample. Then seawater would be poured into a big flask using a filter to extract the bacterial cells. “We wanted to do that on site to capture an immediate snapshot of bacteria as they are living out in the environment,” said Dubinsky. “If we wait to take them to the lab, the bacteria might grow, die or change.”

Then the samples are frozen on dry ice to prevent change. “It’s like Han Solo in ‘Empire Strikes Back,’” quipped Dubinsky. “When we get back to the lab, it’s like ‘Return of the Jedi’ when he’s thawed. Except when we thaw the bacteria in the lab they’re dead and they spill their guts—that’s how we get their DNA. Han Solo survives the thawing process in one piece and goes on to help defeat the Empire.”

~ by Janet Fang on November 26, 2008.

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